AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal.
(2013) Bioinformatics — Vol. 29, n° 16, p. 1963-1969 (2013)
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- Abstract
- MOTIVATION: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights ) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations. RESULTS: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%). AVAILABILITY: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.
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Ambroise, J., Piette, A.-S., Delcorps, C., Rigouts, L., de Jong, B. C., Irenge, L., Robert, A., & Gala, J.-L. (2013). AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal. Bioinformatics, 29(16), 1963-1969. https://doi.org/10.1093/bioinformatics/btt339 (Original work published 2013)